-
2
-
-
0028102267
-
-
S. C. Kowalczykowski, D. A. Dixon, A. K. Eggleston, S. D. Lauder, W. M. Rehrauer, Microbiol. Rev. 58, 401 (1994).
-
(1994)
Microbiol. Rev.
, vol.58
, pp. 401
-
-
Kowalczykowski, S.C.1
Dixon, D.A.2
Eggleston, A.K.3
Lauder, S.D.4
Rehrauer, W.M.5
-
7
-
-
0037443869
-
-
K. Subramanian, W. Rutvisuttinunt, W. Scott, R. S. Myers, Nucl. Acids Res. 31, 1585 (2003).
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 1585
-
-
Subramanian, K.1
Rutvisuttinunt, W.2
Scott, W.3
Myers, R.S.4
-
8
-
-
0032582494
-
-
M. D. Wang et al., Science 282, 902 (1998).
-
(1998)
Science
, vol.282
, pp. 902
-
-
Wang, M.D.1
-
9
-
-
0035909370
-
-
D. E. Smith et al., Nature 413, 748 (2001).
-
(2001)
Nature
, vol.413
, pp. 748
-
-
Smith, D.E.1
-
10
-
-
0037057630
-
-
T. Ha et al., Nature 419, 638 (2002).
-
(2002)
Nature
, vol.419
, pp. 638
-
-
Ha, T.1
-
11
-
-
0141542823
-
-
note
-
Materials and methods are available as supporting material on Science Online.
-
-
-
-
13
-
-
0141431137
-
-
note
-
A force clamp supplies improved resolution over open-loop systems and makes it unnecessary to apply corrections for the elastic compliance of the DNA-motor complex (12). Force clamps based on stage motion, as opposed to those that steer the optical trap by acousto-optic deflectors (28), are well suited to studying slow-moving, processive enzymes, because they afford a greater operating range (>10 μm) together with high precision (∼2 nm) at the cost of reduced feedback loop closure time (∼0.1 s).
-
-
-
-
14
-
-
0141431136
-
-
note
-
The velocity was unchanged by a threefold increase in force from 1 pN (fig. S1A). This insensitivity to external load was observed for several molecules (fig. S1B) and implies that the mechanical translocation step of the reaction cycle is not rate-determining at low loads. A similar finding has been reported for RNA polymerase (8). Force-velocity analysis over a greater range was not possible because tethered complexes failed to support significant loads (>3 pN) for extended periods (∼30s).
-
-
-
-
16
-
-
0141766022
-
-
note
-
Comparing unaligned data sets, we found no significant correlation between the dwell time histograms for forward and backward directions of digestion (11). A cross-correlation analysis yielded a correlation coefficient r = 0.050 [-0.059, +0.159] over the region 605 to 1730 nm, where brackets denote the 95.4% statistical confidence interval determined by a bootstrap resampling analysis. The lack of a single dominant pause in the backward traces prevented us from making a robust backward alignment in that direction. Nevertheless, we attempted an alignment of backward traces, and cross-correlation between aligned forward and backward records yielded a correlation coefficient of r = -0.002 [-0.114, +0.110] over the region 595 to 1760 nm. All cross-correlations were computed over a region selected to contain a minimum of seven records in either direction (table S5).
-
-
-
-
17
-
-
0141431135
-
-
note
-
The estimated numbers of long pauses (>5 s) moving forwards and backwards were 49 and 19, respectively (for pauses >10 s, the corresponding numbers were 19 and 2). Estimates of the number of forward pauses were scaled by a factor of 0.62 to correct for the ratio of the total distance traveled moving forwards to backwards by all molecules scored over this region (675 to 1200 nm).
-
-
-
-
18
-
-
0034737593
-
-
R. J. Davenport, G. J. L. Wuite, R. Landick, C. Bustamante, Science 287, 2497 (2000).
-
(2000)
Science
, vol.287
, pp. 2497
-
-
Davenport, R.J.1
Wuite, G.J.L.2
Landick, R.3
Bustamante, C.4
-
20
-
-
0035905687
-
-
P. R. Bianco et al., Nature 409, 374 (2001).
-
(2001)
Nature
, vol.409
, pp. 374
-
-
Bianco, P.R.1
-
21
-
-
0141766021
-
-
note
-
The single-molecule traces were aligned to 900 nm, which corresponds to a peak in the distribution of shifts necessary to align the traces. The average offset was -2.1 nm. If we aligned the traces so the average offset was O, then the dominant pause moved to 902.1 nm. In either case, the single-molecule data were within 2 nm of the gel-derived location.
-
-
-
-
23
-
-
0028933039
-
-
M. J. Doktycz, M. D. Morris, S. J. Dormady, K. L Beattie, K. B. Jacobson, J. Biol. Chem. 270, 8439 (1995).
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 8439
-
-
Doktycz, M.J.1
Morris, M.D.2
Dormady, S.J.3
Beattie, K.L.4
Jacobson, K.B.5
-
25
-
-
0015457788
-
-
F. W. Stahl, K. D. McMilin, M. M. Stahl, Y. Nozu, Proc. Natl. Acad. Sci. U.S.A. 69, 3598 (1972).
-
(1972)
Proc. Natl. Acad. Sci. U.S.A.
, vol.69
, pp. 3598
-
-
Stahl, F.W.1
McMilin, K.D.2
Stahl, M.M.3
Nozu, Y.4
-
28
-
-
0036284131
-
-
M. J. Lang, C. L. Asbury, J. W. Shaevitz, S. M. Block, Biophys. J. 83, 491 (2002).
-
(2002)
Biophys. J.
, vol.83
, pp. 491
-
-
Lang, M.J.1
Asbury, C.L.2
Shaevitz, J.W.3
Block, S.M.4
-
29
-
-
0141654088
-
-
note
-
We thank K. Neuman and R. Knight for helpful discussions; E. Abbondanzieri for discussions and supplying his pause-finding algorithm; J. Einerson for extensive help with the assays; A. Engh, K. Herbert, and N. Padte for advice and help with sequencing gels; and U. Bali for the generous gift of lambda exonuclease. T.T.P. received support from a Burroughs Wellcome Fund Career Award in the Biomedical Sciences, a Princeton University Materials Institute Fellowship, and NIST. This work was supported by grants from the NIGMS GM 57035 (S.M.B.) and NHGRI HG 011821-01 (P.G.M.).
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